Scientific Papers

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis | Journal of Animal Science and Biotechnology


  • Shi XW, Wang JW, Zeng FT, Qiu XP. Mitochondrial DNA cleavage patterns distinguish independent origin of Chinese domestic geese and Western domestic geese. Biochem Genet. 2006;44:237–45. https://doi.org/10.1007/s10528-006-9028-z.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Eda M, Itahashi Y, Kikuchi H, Sun G, Hsu K-H, Gakuhari T, et al. Multiple lines of evidence of early goose domestication in a 7,000-y-old rice cultivation village in the lower Yangtze River, China. Proc Natl Acad Sci U S A. 2022;119(12):e2117064119. https://doi.org/10.1073/pnas.2117064119.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li HF, Zhu WQ, Chen KW, H Y, Xu WJ, Song W. Two maternal origins of Chinese domestic goose. Poult Sci. 2011;90(12):2705–10. https://doi.org/10.3382/ps.2011-01425.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Wen J, Li H, Wang H, Yu J, Zhu T, Zhang J, et al. Origins, timing and introgression of domestic geese revealed by whole genome data. J Anim Sci Biotechnol. 2023;14:26. https://doi.org/10.1186/s40104-022-00826-9.

    Article 
    CAS 

    Google Scholar
     

  • Boz MA, Sarica M, Yamak US. Production traits of artificially and naturally hatched geese in intensive and free-range systems: I. Growth traits Br Poult Sci. 2017;58(2):132–8. https://doi.org/10.1080/00071668.2016.1261997.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kozák J. Variations of geese under domestication. Worlds Poult Sci J. 2019;75(2):247–60. https://doi.org/10.1017/S0043933919000023.

    Article 

    Google Scholar
     

  • Zhao Q, Lin Z, Chen J, Xie Z, Wang J, Feng K, et al. Chromosome-level genome assembly of goose provides insight into the adaptation and growth of local goose breeds. GigaScience. 2023;12:giad003. https://doi.org/10.1093/gigascience/giad003.

    Article 
    CAS 
    PubMed Central 

    Google Scholar
     

  • Lu L, Chen Y, Wang Z, Li X, Chen W, Tao Z, et al. The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver. Genome Biol. 2015;16:89. https://doi.org/10.1186/s13059-015-0652-y.

  • Gao GL, Zhao XZ, Li Q, He C, Zhao WJ, Liu SY, et al. Genome and metagenome analyses reveal adaptive evolution of the host and interaction with the gut microbiota in the goose. Sci Rep. 2016;6:32961. https://doi.org/10.1038/srep32961.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang YW, Zhang B, Zhang Y, Nie RX, Zhang J, Shang P, et al. Chromosome-level genome assembly of the bar-headed goose (Anser indicus). Sci Data. 2022;9:668. https://doi.org/10.1038/s41597-022-01801-9.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ouyang J, Zheng SM, Huang M, Tang HB, Qiu XH, Chen SJ, et al. Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese. Commun Biol. 2022;5:1191. https://doi.org/10.1038/s42003-022-04125-x.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang YH, Ni HY, Xie HL, Yin YJ, Zheng JL, Dong LP, et al. De novo assembly of a wild swan goose (Anser cygnoides) genome. Anim Genet. 2022;53(6):878–80. https://doi.org/10.1111/age.13262.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li Y, Gao GL, Lin Y, Hu SL, Luo Y, Wang GS, et al. Pacific biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome. GigaScience. 2020;9(10):giaa114. https://doi.org/10.1093/gigascience/giaa114.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Karawita AC, Cheng Y, Chew KY, Challagulla A, Kraus R, Mueller RC, et al. The swan genome and transcriptome, it is not all black and white. Genome Biol. 2023;24:13. https://doi.org/10.1186/s13059-022-02838-0.

    Article 

    Google Scholar
     

  • Xi Y, Wang L, Liu HH, Ma SC, Li YY, Li L, et al. A 14-bp insertion in endothelin receptor B-like (EDNRB2) is associated with white plumage in Chinese geese. BMC Genomics. 2020;21:162. https://doi.org/10.1186/s12864-020-6562-8.

  • Gao GL, Gao DF, Zhao XZ, Xu SS, Zhang KS, Wu R, et al. Genome-wide association study-based identification of SNPs and haplotypes associated with goose reproductive performance and egg quality. Front Genet. 2021;12:602583. https://doi.org/10.3389/fgene.2021.602583.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhao Q, Chen JP, Zhang XH, Xu ZY, Lin ZP, Li HX, et al. Genome-wide association analysis reveals key genes responsible for egg production of lion head goose. Front Genet. 2020;10:1391. https://doi.org/10.3389/fgene.2019.01391.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Heikkinen ME, Ruokonen M, White TA, Alexander MM, Gündüz İ, Dobney KM, et al. Long-term reciprocal gene flow in wild and domestic geese reveals complex domestication history. G3 (Bethesda). 2020;10(9):3061–70. https://doi.org/10.1534/g3.120.400886.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Deng Y, Hu SQ, Luo CL, Ouyang QY, Li L, Ma JM, et al. Integrative analysis of histomorphology, transcriptome and whole genome resequencing identified DIO2 gene as a crucial gene for the protuberant knob located on forehead in geese. BMC Genomics. 2021;22:487. https://doi.org/10.1186/s12864-021-07822-9.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wen J, Shao P, Chen Y, Wang L, Lv X, Yang W, et al. Genomic scan revealed KIT gene underlying white/gray plumage color in Chinese domestic geese. Anim Genet. 2021;52(3):356–60. https://doi.org/10.1111/age.13050.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zheng S, Ouyang J, Liu S, Tang H, Xiong Y, Yan X, et al. Genomic signatures reveal selection in Lingxian white goose. Poult Sci. 2023;102(1):102269. https://doi.org/10.1016/j.psj.2022.102269.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chen J, Zhang S, Chen G, Deng X, Zhang D, Wen H, et al. Transcriptome sequencing reveals pathways related to proliferation and differentiation of shitou goose myoblasts. Animals (Basel). 2022;12(21):2956. https://doi.org/10.3390/ani12212956.

    Article 
    PubMed 

    Google Scholar
     

  • Hu M, Jin H, Wu J, Zhou X, Yang S, Zhao A, et al. Identification of the differentially expressed genes in the leg muscles of Zhedong white geese (Anser cygnoides) reared under different photoperiods. Poult Sci. 2022;101(12):102193. https://doi.org/10.1016/j.psj.2022.102193.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ouyang Q, Hu S, Wang G, Hu J, Zhang J, Li L, et al. Comparative transcriptome analysis suggests key roles for 5-hydroxytryptamlne receptors in control of goose egg production. Genes (Basel). 2020;11(4):455. https://doi.org/10.3390/genes11040455.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Gong Y, Li Y, Liu X, Ma Y, Jiang L. A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals? J Anim Sci Biotechnol. 2023;14:73. https://doi.org/10.1186/s40104-023-00860-1.

    Article 
    CAS 

    Google Scholar
     

  • Talenti A, Powell J, Hemmink JD, Cook EA, Wragg D, Jayaraman S, et al. A cattle graph genome incorporating global breed diversity. Nat Commun. 2022;13:910. https://doi.org/10.1038/s41467-022-28605-0.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li R, Gong M, Zhang X, Wang F, Liu Z, Zhang L, et al. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Res. 2023;33(3):463–77. https://www.genome.org/cgi/doi/10.1101/gr.277372.122.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jiang YF, Wang S, Wang CL, Xu RH, Wang WW, Jiang Y, et al. Pangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs. iScience. 2023;26(3):106119. https://doi.org/10.1016/j.isci.2023.106119.

  • Wang K, Hu H, Tian Y, Li J, Scheben A, Zhang C, et al. The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size. Mol Biol Evol. 2021;38(11):5066–81. https://doi.org/10.1093/molbev/msab231.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tian X, Li R, Fu W, Li Y, Wang X, Li M, et al. Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data. Sci China Life Sci. 2020;63:750–63. https://doi.org/10.1007/s11427-019-9551-7.

    Article 
    PubMed 

    Google Scholar
     

  • Zhou Y, Yang L, Han X, Han J, Hu Y, Li F, et al. Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history. Genome Res. 2022;32(8):1585–601 https://www.genome.org/cgi/doi/10.1101/gr.276550.122.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ottenburghs J, Megens HJ, Kraus RHS, Van Hooft P, Van Wieren SE, Crooijmans RPMA, et al. A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evol Biol. 2017;17:201. https://doi.org/10.1186/s12862-017-1048-2.

    Article 

    Google Scholar
     

  • Díez-Del-Molino D, Von Seth J, Gyllenstrand N, Widemo F, Liljebäck N, Svensson M, et al. Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose. Sci Rep. 2020;10:18347. https://doi.org/10.1038/s41598-020-75315-y.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ottenburghs J, Honka J, Müskens GJDM, Ellegren H. Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation. Heredity (Edinb). 2020;125(1–2):73–84. https://doi.org/10.1038/s41437-020-0322-z.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Kaiqi W, Weiran H, Yang Z, Qi X, Guohong C. Principal component analysis of body size, reproductive traits and ecological characteristics on Chinese indigenous Goose Breeds. J Sichuan Univ. 2021;38(02):225–33. https://doi.org/10.16036/j.issn.1000-2650.2020.02.015.

    Article 

    Google Scholar
     

  • Gao GL, Chen PP, Zhou C, Zhao XZ, Zhang KS, Wu R, et al. Genome-wide association study for reproduction-related traits in Chinese domestic goose. Br Poult Sci. 2022;63(6):754–60. https://doi.org/10.1080/00071668.2022.2096402.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60. https://doi.org/10.1093/bioinformatics/btp324.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Danecek P, Auton A, Abecasis G, Albers CA, Banks E, Depristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8. https://doi.org/10.1093/bioinformatics/btr330.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6(2):80–92. https://doi.org/10.4161/fly.19695.

  • Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, Von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37(5):1530–4. https://doi.org/10.1093/molbev/msaa015.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Alexander DH, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 2009;19(9):1655–64. http://www.genome.org/cgi/doi/10.1101/gr.094052.109.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pickrell J, Pritchard J. Inference of population splits and mixtures from genome-wide allele frequency data. Nat Prec. 2012. https://doi.org/10.1038/npre.2012.6956.1.

  • Cai X, Sun X, Xu C, Sun H, Wang X, Ge C, et al. Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits. Nat Commun. 2021;12:7246. https://doi.org/10.1038/s41467-021-27432-z.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res. 2010;20(3):393–402. http://www.genome.org/cgi/doi/10.1101/gr.100545.109.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sherman RM, Forman J, Antonescu V, Puiu D, Daya M, Rafaels N, et al. Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nat Genet. 2019;51(1):30–5. https://doi.org/10.1038/s41588-018-0273-y.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013;29(21):2669–77. https://doi.org/10.1093/bioinformatics/btt476.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: a fast and versatile genome alignment system. PLoS Comput Biol. 2018;14(1):e1005944. https://doi.org/10.1371/journal.pcbi.1005944.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012;28(23):3150–2. https://doi.org/10.1093/bioinformatics/bts565.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019;20:257. https://doi.org/10.1186/s13059-019-1891-0.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tahir UI, Qamar M, Zhu X, Xing F, Chen LL. ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline. Bioinformatics. 2019;35(20):4156–8. https://doi.org/10.1093/bioinformatics/btz168.

    Article 
    CAS 

    Google Scholar
     

  • Song JM, Guan Z, Hu J, Guo C, Yang Z, Wang S, et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nat Plants. 2020;6(1):34–45. https://doi.org/10.1038/s41477-019-0577-7.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gao GL, Hu SL, Zhang KS, Wang HW, Xie YH, Zhang CL, et al. Genome-wide gene expression profiles reveal distinct molecular characteristics of the goose granulosa cells. Front Genet. 2021;12:786287. https://doi.org/10.3389/fgene.2021.786287.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang G, Jin L, Li Y, Tang Q, Hu S, Xu H, et al. Transcriptomic analysis between normal and high-intake feeding geese provides insight into adipose deposition and susceptibility to fatty liver in migratory birds. BMC Genomics. 2019;20:372. https://doi.org/10.1186/s12864-019-5765-3.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen N. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. 2004;5(1):4–10. https://doi.org/10.1002/0471250953.bi0410s25.

    Article 

    Google Scholar
     

  • Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A. 2020;117(17):9451–7. https://doi.org/10.1073/pnas.1921046117.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27(2):573–80. https://doi.org/10.1093/nar/27.2.573.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019;37(8):907–15. https://doi.org/10.1038/s41587-019-0201-4.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data. Nat Biotechnol. 2011;29(7):644–52. https://doi.org/10.1038/nbt.1883.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Holt C, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics. 2011;12:491. https://doi.org/10.1186/1471-2105-12-491.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006;34(suppl_2):W435–9. https://doi.org/10.1093/nar/gkl200.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9. https://doi.org/10.1038/nmeth.1923.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Golicz AA, Martinez PA, Zander M, Patel DA, Van De Wouw AP, Visendi P, et al. Gene loss in the fungal canola pathogen Leptosphaeria maculans. Funct Integr Genomics. 2015;15:189–96. https://doi.org/10.1007/s10142-014-0412-1.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74. https://doi.org/10.1093/molbev/msu300.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Hubisz MJ, Falush D, Stephens M, Pritchard JK. Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour. 2009;9(5):1322–32. https://doi.org/10.1111/j.1755-0998.2009.02591.x.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu X, Huang M, Fan B, Buckler ES, Zhang Z. Iterative usage of fixed and random effect models for powerful and efficient genome-wide association studies. PLoS Genet. 2016;12(2):e1005767. https://doi.org/10.1371/journal.pgen.1005767.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet. 2011;88(1):76–82. https://doi.org/10.1016/j.ajhg.2010.11.011.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li X, Shi Z, Gao J, Wang X, Guo K. CandiHap: a haplotype analysis toolkit for natural variation study. Mol Breed. 2023;43(3):21. https://doi.org/10.1007/s11032-023-01366-4.

    Article 
    PubMed 

    Google Scholar
     

  • Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30(7):923–30. https://doi.org/10.1093/bioinformatics/btt656.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Conesa A, Nueda MJ, Ferrer A, Talón M. maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics. 2006;22(9):1096–102. https://doi.org/10.1093/bioinformatics/btl056.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. https://doi.org/10.1186/s13059-014-0550-8.

    Article 
    CAS 

    Google Scholar
     

  • Mclaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. The ensembl variant effect predictor. Genome Biol. 2016;17:122. https://doi.org/10.1186/s13059-016-0974-4.

    Article 
    CAS 

    Google Scholar
     

  • Heikkinen M, Ruokonen M, Alexander M, Aspi J, Pyhäjärvi T, Searle JB. Relationship between wild greylag and European domestic geese based on mitochondrial DNA. Anim Genet. 2015;46(5):485–97. https://doi.org/10.1111/age.12319.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ottenburghs J, Van Hooft P, Van Wieren SE, Ydenberg RC, Prins HH. Hybridization in geese: a review. Front Zool. 2016;13:20. https://doi.org/10.1186/s12983-016-0153-1.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang MS, Zhang JJ, Guo X, Li M, Meyer R, Ashari H, et al. Large-scale genomic analysis reveals the genetic cost of chicken domestication. BMC Biol. 2021;19:118. https://doi.org/10.1186/s12915-021-01052-x.

    Article 
    CAS 

    Google Scholar
     

  • Hu Y, Yu H, Shaw G, Renfree MB, Pask A. Differential roles of TGIF family genes in mammalian reproduction. BMC Dev Biol. 2011;11:58. https://doi.org/10.1186/1471-213X-11-58.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang Z, He X, Liu Q, Tang J, Di R, Chu M. TGIF1 and SF1 polymorphisms are associated with litter size in Small Tail Han sheep. Reprod Domest Anim. 2020;55(9):1145–53. https://doi.org/10.1111/rda.13753.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Prota AE, Magiera MM, Kuijpers M, Bargsten K, Frey D, Wieser M, et al. Structural basis of tubulin tyrosination by tubulin tyrosine ligase. J Cell Biol. 2013;200(3):259–70. https://doi.org/10.1083/jcb.201211017.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu Z, Sun C, Yan Y, Li G, Shi F, Wu G, et al. Genetic variations for egg quality of chickens at late laying period revealed by genome-wide association study. Sci Rep. 2018;8:10832. https://doi.org/10.1038/s41598-018-29162-7.

    Article 
    CAS 

    Google Scholar
     

  • Gao JF, Xu W, Zeng T, Tian Y, Wu CQ, Liu SZ, et al. Genome-wide association study of egg-laying traits and egg quality in LingKun chickens. Front Vet Sci. 2022;9:877739. https://doi.org/10.3389/fvets.2022.877739.

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang GX, Fan QC, Wang JY, Zhang T, Xue Q, Shi HQ. Genome-wide association study on reproductive traits in Jinghai Yellow Chicken. Anim Reprod Sci. 2015;163:30–4. https://doi.org/10.1016/j.anireprosci.2015.09.011.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ghebremicael SB, Hasenstein JR, Lamont SJ. Association of interleukin-10 cluster genes and Salmonella response in the chicken. Poult Sci. 2008;87(1):22–6. https://doi.org/10.3382/ps.2007-00259.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Schindler JF, Godbey A, Hood WF, Bolten SL, Broadus RM, Kasten TP, et al. Examination of the kinetic mechanism of mitogen-activated protein kinase activated protein kinase-2. Biochim Biophys Acta. 2002;1598(1–2):88–97. https://doi.org/10.1016/S0167-4838(02)00340-0.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Ning B, Huang J, Xu H, Lou Y, Wang W, Mu F, et al. Genomic organization, intragenic tandem duplication, and expression analysis of chicken TGFBR2 gene. Poult Sci. 2022;101(12):102169. https://doi.org/10.1016/j.psj.2022.102169.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Michelini S, Amato B, Ricci M, Serrani R, Veselenyiova D, Kenanoglu S, et al. SVEP1 is important for morphogenesis of lymphatic system: possible implications in lymphedema. Lymphology. 2021;54(1):12–22. https://doi.org/10.7554/eLife.82969.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Jung IH, Elenbaas JS, Alisio A, Santana K, Young EP, Kang CJ, et al. SVEP1 is a human coronary artery disease locus that promotes atherosclerosis. Sci Transl Med. 2021;13(586):eabe0357. https://doi.org/10.1126/scitranslmed.abe0357.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li M, Sun C, Xu N, Bian P, Tian X, Wang X, et al. De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on microchromosomes and subtelomeric regions. Mol Biol Evol. 2022;39(4):msac066. https://doi.org/10.1093/molbev/msac066.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhu F, Yin ZT, Wang Z, Smith J, Zhang F, Martin F, et al. Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. Nat Commun. 2021;12:5932. https://doi.org/10.1038/s41467-021-26272-1.

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu Y, Du H, Li P, Shen Y, Peng H, Liu S, et al. Pan-genome of wild and cultivated soybeans. Cell. 2020;182(1):162–76.e113. https://doi.org/10.1016/j.cell.2020.05.023.

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Qin P, Lu H, Du H, Wang H, Chen W, Chen Z, et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations. Cell. 2021;184(13):3542–58.e16. https://doi.org/10.1016/j.cell.2021.04.046.

    Article 
    CAS 
    PubMed 

    Google Scholar
     



  • Source link